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Many people have reported problems with transferring lots of ebooks in one go to their Kobo.
Try removing all the books and then add them back in batches. Start with small batches, ie 20 books at a time, and check that all books show up after each batch.
I know it's a pain but using this method usually identifies any bad ebooks and it makes it easier to identify which ebook the Kobo is chocking on.
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